Individualized CRISPR Approaches to Advance Next-Gen Probiotics in Microbiome Engineering

Individualized CRISPR Approaches to Advance Next-Gen Probiotics in Microbiome Engineering ...

Researchers have made advances in understanding and manipulating an essential human gut bacteria, Bifidobacterium, which is often used in probiotics that help maintain healthy microbiomes. The research opens the way for future-generation probiotics and underscores the need to develop individual CRISPR-based engineering strategies for certain bacteria.

Rodolphe Barrangou, PhD, the Todd R. Klaenhammer distinguished professor of food, bioprocessing, and nutrition sciences at North Carolina State University, was published in the Proceedings of the National Academy of Sciences of the United States of America (CRISPR-based genome editing in Bifidobacterium).

CRISPR-Cas genome editing algorithms are used in Barrangous labs to study and improve beneficial bacteria in fermented foods and probiotics. We are turning to more finicky bacteria, likeBifidobacterium, because it is harder to grow and harder to work with than others.

Bifidobacterium's experimental development has been hampered by its complex cell wall and an abundance of restriction-modification mechanisms, among other factors. However, Meichen (Echo) Pan, a doctoral student in the Barrangous lab and the first author of the paper, discovered that these bacteria are used in many probioticsproducts with live microorganisms that promote health.

According to Pan, Bifidobacterium andLactobacillus are the top two genera in commercial probiotics. There are huge opportunities and needs from the probiotic business to better understand these bacteria, to enhance their probiotic capabilities, and to maximize their potential health benefits.

Nevertheless, [Bifidobacterium] is much more difficult to manipulate than Lactobacillus, according to the author. It's critical to find molecular tools that work in Bifidobacterium for engineering strains with improved probiotic characteristics, as well as for developing biotherapeutic applications.

Although Bifidobacterium was known to possess CRISPR-Cas systems, CRISPR-based genome editing was still not achieved. In the new research, the researchers used one of the bacteria's native CRISPR-Cas systemsa relatively understudied type I-G systemand an exogenous base editor to engineer Bifidobacterium.

CRISPR is used on the bench these days, and individuals, including scientists like me, are starting to take it for granted, according to Pan. Not to trivialize engineering E. coli, but using CRISPR to genetically modify non-canonical bacteria such as Bifidobacterium is a whole new ball game.

Bifidobacteriumto tetracycline, a common antibiotic, was re-sensitized by their tailored CRISPR-based strategy. It's conceptually and practically critical because bacteria can transfer antibacterial resistance to other bacteria in the gut.

Barrangou stated that there are other possibilities for enhancing Bifidobacterium's probiotic capacity, including the possibility to enhance infants' Bifidobacterium predominate and promote life-long gut microbiome homeostasis. Another possibility is to modify the molecular interaction between host epithelial and immune cells to reduce inflammation.

The researchers then extended their research, uncovering epigenetic patterns that differed among strains, despite their relative genomic homogeneity, that may contribute to variability in editing efficiency.

Barrangou concluded that this was a fairly unexpected but obviously practically significant finding. At a time when we all recognize the value of personalized medicine and nutrition and also appreciate how the epigenome shapes much of the genome biology and cellular function, it is important to recognize that even cells that are 99.9% genetically identical may require customized genome editing techniques.

Barrangou noted that the researchers' strategy might be applied to other bacteria. There are many other organisms in the human gut microbiome and a slew of bacteria that are suitable for this type of approach in environmental contexts, including water and soil.

Most research is done on model organisms because they are quick and easy, but imagine how much more we might learn by studying non-model organisms that actually matter and affect our health, Pan said. I am so proud to be a part of a research group that is willing to accept challenges and always striving to conquer.

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